I'm running Jenkins 2.401.2 on Ubuntu 22.04 LTS. Once a month, I see logs under tasks deleting some of my workspaces. 

cat /var/lib/jenkins/logs/tasks/Workspace\ clean-up.log | grep Deleting
Deleting /var/lib/jenkins/workspace/<Path to my workspace>

To prevent it, I uninstalled the Workspace cleanup plugin and added the following flag: 
JAVA_ARGS="-Dhudson.model.WorkspaceCleanupThread.disabled=true"

Even after taking these actions, my workspaces are being deleted.